[English] 日本語
Yorodumi
- PDB-2vrw: Critical structural role for the PH and C1 domains of the Vav1 ex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vrw
TitleCritical structural role for the PH and C1 domains of the Vav1 exchange factor
Components
  • PROTO-ONCOGENE VAV
  • RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
KeywordsSIGNALING PROTEIN / LIPOPROTEIN / GTP-BINDING / METAL-BINDING / PROTO-ONCOGENE / PHOSPHOPROTEIN / EXCHANGE FACTOR / RAC / VAV / GTPASE / MEMBRANE / SH2 DOMAIN / SH3 DOMAIN / METHYLATION / ZINC-FINGER / PRENYLATION / GUANINE-NUCLEOTIDE RELEASING FACTOR / PHORBOL-ESTER BINDING / ADP-RIBOSYLATION / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


Azathioprine ADME / CD28 dependent Vav1 pathway / RAC2 GTPase cycle / Erythropoietin activates RAS / GPVI-mediated activation cascade / RHOA GTPase cycle / FCERI mediated MAPK activation / NRAGE signals death through JNK / Signaling by SCF-KIT / RAC1 GTPase cycle ...Azathioprine ADME / CD28 dependent Vav1 pathway / RAC2 GTPase cycle / Erythropoietin activates RAS / GPVI-mediated activation cascade / RHOA GTPase cycle / FCERI mediated MAPK activation / NRAGE signals death through JNK / Signaling by SCF-KIT / RAC1 GTPase cycle / RHOG GTPase cycle / VEGFR2 mediated vascular permeability / regulation of respiratory burst / FCERI mediated Ca+2 mobilization / phosphorylation-dependent protein binding / negative regulation of interleukin-23 production / G alpha (12/13) signalling events / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / PIP3 activates AKT signaling / NADPH oxidase complex / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / Regulation of signaling by CBL / engulfment of apoptotic cell / Regulation of actin dynamics for phagocytic cup formation / Inactivation of CDC42 and RAC1 / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Interleukin-3, Interleukin-5 and GM-CSF signaling / cortical cytoskeleton organization / respiratory burst / hepatocyte growth factor receptor signaling pathway / ruffle organization / cell projection assembly / thioesterase binding / negative regulation of fibroblast migration / VEGFA-VEGFR2 Pathway / regulation of stress fiber assembly / RHO GTPases activate CIT / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / regulation of nitric oxide biosynthetic process / PCP/CE pathway / motor neuron axon guidance / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / positive regulation of neutrophil chemotaxis / Azathioprine ADME / Activation of RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / MET activates RAP1 and RAC1 / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / positive regulation of Rho protein signal transduction / establishment or maintenance of cell polarity / regulation of cell size / DSCAM interactions / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / NRAGE signals death through JNK / positive regulation of natural killer cell mediated cytotoxicity / Rac protein signal transduction / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / T cell differentiation / positive regulation of cell adhesion / RHO GTPases Activate NADPH Oxidases / RHO GTPases Activate WASPs and WAVEs / anatomical structure morphogenesis / RHO GTPases activate IQGAPs / localization / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / phagocytosis / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / reactive oxygen species metabolic process / actin filament polymerization / phosphotyrosine residue binding
Similarity search - Function
VAV1 protein, second SH3 domain / VAV1 protein, first SH3 domain / VAV1, SH2 domain / Vav, PH domain / Smooth muscle protein/calponin / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / CAMSAP CH domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Dbl Homology Domain; Chain A / Dbl homology (DH) domain ...VAV1 protein, second SH3 domain / VAV1 protein, first SH3 domain / VAV1, SH2 domain / Vav, PH domain / Smooth muscle protein/calponin / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / CAMSAP CH domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Small GTPase Rho / Calponin homology domain / small GTPase Rho family profile. / Phorbol esters/diacylglycerol binding domain (C1 domain) / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / SH3 domain / Small GTPase / Ras family / Rab subfamily of small GTPases / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / Src homology 3 domains / SH2 domain / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Proto-oncogene vav / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsRapley, J. / Tybulewicz, V. / Rittinger, K.
CitationJournal: Embo Rep. / Year: 2008
Title: Crucial Structural Role for the Ph and C1 Domains of the Vav1 Exchange Factor.
Authors: Rapley, J. / Tybulewicz, V. / Rittinger, K.
History
DepositionApr 16, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
B: PROTO-ONCOGENE VAV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0934
Polymers67,9622
Non-polymers1312
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-15.7 kcal/mol
Surface area32450 Å2
MethodPQS
Unit cell
Length a, b, c (Å)122.763, 62.143, 103.281
Angle α, β, γ (deg.)90.00, 118.80, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 / P21-RAC1 / RAS- LIKE PROTEIN TC25 / CELL MIGRATION-INDUCING GENE 5 PROTEIN / RAC1


Mass: 20462.746 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-4T1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P63000
#2: Protein PROTO-ONCOGENE VAV / P95VAV / VAV1


Mass: 47499.234 Da / Num. of mol.: 1 / Fragment: RESIDUES 170-575
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET24B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P27870
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 50.91 % / Description: NONE
Crystal growpH: 9 / Details: 100MM BICINE PH9.0 10% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.117
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.117 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 57653 / % possible obs: 99.2 % / Observed criterion σ(I): 5 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.2
Reflection shellResolution: 1.85→1.93 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.8 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→15 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.338 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2937 5.1 %RANDOM
Rwork0.203 ---
obs0.205 54863 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.36 Å2
2---0.58 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4400 0 2 471 4873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224498
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0311.9676069
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2425545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94323.917217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54615835
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6141534
X-RAY DIFFRACTIONr_chiral_restr0.0740.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023377
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.22151
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.23089
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2420
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5421.52821
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.90124400
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.46331901
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3284.51668
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.283 202
Rwork0.259 3906
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9408-0.77140.77951.3813-0.10471.1312-0.1580.15190.1391-0.05340.03930.0722-0.11390.04030.1187-0.0301-0.0295-0.0283-0.03570.0407-0.0252-8.514-28.59216.8848
20.52880.60080.44491.22270.29230.58680.02010.0040.01210.04280.01580.03220.0312-0.0406-0.0358-0.019-0.00620.0126-0.03110.0042-0.0337-1.0518-43.234134.7584
31.1124-0.1691-0.47190.61040.19153.19940.02510.1084-0.0379-0.053-0.04390.05880.23260.18550.0188-0.01070.01250.0067-0.0356-0.0405-0.054922.7588-57.45881.9478
43.90541.0536-0.50632.17450.74881.5486-0.07920.0040.01340.0070.0644-0.05330.01370.04380.0148-0.06510.0006-0.0076-0.0341-0.0089-0.0228.3111-45.878424.8559
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 177
2X-RAY DIFFRACTION2B190 - 373
3X-RAY DIFFRACTION3B374 - 508
4X-RAY DIFFRACTION4B509 - 564

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more